Small correction in file / folder naming for batch correction.

R/correct_batch_effect.R

@@ -49,6 +49,24 @@ correct_batch_effect <- function(eset,
     }
   }
 
+  # We remove the probes that have 0 variance accross the samples for each batch.
+  # Not doing so will prevent Combat from running.
+  exp_data         <- Biobase::exprs(eset)
+  clean_probe_list <- rownames(exp_data)
+  for (b in unique(batch_data$Batch)) {
+    # We take care of batch b.
+    samples_in_batch <- which(batch_data$Batch == b)
+    exp_data_batch <- exp_data[, samples_in_batch]
+    probe_vars     <- apply(exp_data_batch, 1, var)
+    probe_var_0    <- names(probe_vars[probe_vars == 0])
+    if (length(probe_var_0) > 0) {
+      clean_probe_list <- setdiff(clean_probe_list, probe_var_0)
+    }
+  }
+  remove(b, samples_in_batch, exp_data_batch, probe_vars, probe_var_0)
+  eset <- Biobase::ExpressionSet(exp_data[clean_probe_list, ])
+  remove(exp_data, clean_probe_list)
+
   # ComBat corrects for the batch effect.
   data_bc <- sva::ComBat(dat       = Biobase::exprs(eset),
                          batch     = batch_data$Batch,

R/preprocess_data_affymetrix_gcrma.R

@@ -90,7 +90,7 @@ preprocess_data_affymetrix_gcrma <- function(input_data_dir, output_data_files,
 
   # We return the created ESET(s).
   if (batch_correction == "BOTH") {
-    return(list(eset, eset_bc))
+    return(list(eset_bc, eset))
   } else {
     return(eset)
   }

R/preprocess_data_affymetrix_scan.R

@@ -89,7 +89,7 @@ preprocess_data_affymetrix_scan <- function(input_data_dir, output_data_files,
 
   # We return the created ESET(s).
   if (batch_correction == "BOTH") {
-    return(list(eset, eset_bc))
+    return(list(eset_bc, eset))
   } else {
     return(eset)
   }

R/preprocess_data_agilent_limma.R

@@ -115,7 +115,7 @@ preprocess_data_agilent_limma <- function(input_data_dir, output_data_files,
 
   # We return the created ESET(s).
   if (batch_correction == "BOTH") {
-    return(list(eset, eset_bc))
+    return(list(eset_bc, eset))
   } else {
     return(eset)
   }

R/preprocess_data_illumina_beadarray.R

@@ -132,7 +132,7 @@ preprocess_data_illumina_beadarray <- function(input_data_dir, output_data_files
 
   # We return the created ESET(s).
   if (batch_correction == "BOTH") {
-    return(list(eset, eset_bc))
+    return(list(eset_bc, eset))
   } else {
     return(eset)
   }